PCNX1
Basic information
Region (hg38): 14:70907405-71115382
Previous symbols: [ "PCNXL1", "PCNX" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 10 | |||||
missense | 19 | 26 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 1 | |||||
Total | 0 | 0 | 19 | 8 | 10 |
Variants in PCNX1
This is a list of pathogenic ClinVar variants found in the PCNX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-70907862-G-C | not specified | Uncertain significance (Nov 16, 2021) | ||
14-70907901-C-T | Likely benign (Apr 01, 2022) | |||
14-70946990-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
14-70946994-A-C | Benign (Oct 09, 2018) | |||
14-70947065-C-G | Likely benign (Apr 01, 2022) | |||
14-70976988-C-T | Likely benign (Apr 30, 2018) | |||
14-70977031-T-C | Likely benign (Jun 01, 2022) | |||
14-70977098-C-G | not specified | Uncertain significance (Nov 08, 2021) | ||
14-70977099-T-G | Benign (Jan 01, 2023) | |||
14-70977260-G-A | not specified | Uncertain significance (Nov 15, 2021) | ||
14-70977684-T-C | Benign (Jul 04, 2018) | |||
14-70977710-C-T | not specified | Likely benign (Oct 27, 2021) | ||
14-70977749-C-G | Benign (Dec 31, 2019) | |||
14-70978076-A-G | not specified | Uncertain significance (Nov 16, 2021) | ||
14-70978120-A-C | not specified | Uncertain significance (Jun 11, 2021) | ||
14-70978353-G-A | Benign (Dec 31, 2019) | |||
14-70978354-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
14-70978516-G-C | not specified | Uncertain significance (Nov 12, 2021) | ||
14-70978539-A-G | Benign (May 03, 2018) | |||
14-70988600-G-A | Likely benign (May 18, 2018) | |||
14-70988677-T-C | Benign (Oct 09, 2018) | |||
14-70988692-C-T | not specified | Uncertain significance (Oct 29, 2021) | ||
14-71009651-C-G | not specified | Uncertain significance (Jul 27, 2021) | ||
14-71019061-G-T | Malignant tumor of prostate | Uncertain significance (-) | ||
14-71033444-C-G | not specified | Uncertain significance (Nov 15, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PCNX1 | protein_coding | protein_coding | ENST00000304743 | 36 | 207978 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.00000139 | 125706 | 0 | 42 | 125748 | 0.000167 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.43 | 1124 | 1.27e+3 | 0.887 | 0.0000687 | 15288 |
Missense in Polyphen | 408 | 579.56 | 0.70398 | 6918 | ||
Synonymous | -0.375 | 474 | 464 | 1.02 | 0.0000236 | 4690 |
Loss of Function | 8.35 | 17 | 113 | 0.151 | 0.00000674 | 1259 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000268 | 0.000268 |
Ashkenazi Jewish | 0.000404 | 0.000397 |
East Asian | 0.000218 | 0.000163 |
Finnish | 0.000140 | 0.000139 |
European (Non-Finnish) | 0.000179 | 0.000176 |
Middle Eastern | 0.000218 | 0.000163 |
South Asian | 0.000163 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- rvis_EVS
- -1.95
- rvis_percentile_EVS
- 1.87
Haploinsufficiency Scores
- pHI
- 0.126
- hipred
- N
- hipred_score
- 0.466
- ghis
- 0.595
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Pcnx
- Phenotype
Gene ontology
- Biological process
- Cellular component
- integral component of membrane
- Molecular function